Aether 2 is a continuation of the Aether with new content and a new approach to dungeons, Aether Legacy is Aether 1, in a nutshell. If you liked the way the Aether was but for modern versions of the game use Aether Legacy. If you want the new approach to the Aether or new content than use Aether 2. I could go 'deeper' but I think that says enough if your familiar with the mod's differences at least.

I'd check out their mod pages so you can see the differences rather than me stating what they have when the mod pages give a good enough idea of what your getting into with either mod or you could try out both in 2 instances and see which you like better. I haven't used Aether 2 before but I know of it briefly from videos and what the mod page states. While Aether Legacy I am more familiar with in certain areas but not completely.

I'm not going to state which is better if it's up to you, since I don't know if you want the new content or challenge, or the old school approach I can't really say for sure, both are good for different reasons.